Dr. David McKeown sent out the alert early Thursday morning, just ahead of the expected arrival of a string of hot days.
The alert cautions people to take it easy in the heat, especially anyone with breathing problems.
It also advises people to check on those who might be vulnerable during the heat.
Environment Canada said a "very hot air mass" from the midwestern U.S. was to move into southern Ontario on Thursday.
Humidex values "are expected to be generally in the mid to upper thirties over the weekend," the weather agency said.
"So it's hot and sticky, but not as hot and sticky as our last round," said CBC meteorologist Johanna Wagstaffe, referring to the heat wave that swept through the GTA less than two weeks ago.
"It's kind of a 'spare the air' day" both Thursday and Friday, she said. "It's definitely [a time to] take precautions for people who have problems in the heat and the humidity and breathing problems, because of the pollution."
The GTA should expect "some sizzling temperatures to start the long weekend," said Wagstaffe.
The expected high in Toronto for Friday and Saturday is 32 C.